Hi,
I'm modelling G-protein coupled receptors using rhodopsin as a template.
When I compare the Ramachandran plot of the models vs that of rhodopsin,
the models have much more ideal helices than the rhodopsin X-ray structure
(2.8 A).
Is this because:
1) The homology is relatively low (20-30%) and the distance constraints
receive a low weight in the pdf function??
2) The helices in rhodopsin are less regular than the globular proteins
used in the pdf parametrization??
3) None of the above...
Sincerely,
Dan
--
Dan Thomas Major (at Dr. B. Fischer's lab)
Bar-Ilan University
Ramat-Gan, Israel
Phone: 972-3-5317785
Fax: 972-3-5348730